Its not just conference champions in the bye positions for any other football tournament (or any other NCAA tournament) to answer your question. In EVERY other sport, they get the best teams in there, and then rank them accordingly. So #15 wont get a bye while #2 or #3 doesnt. So that makes all of what you said moot.
Yeah, well ... this is only a big deal because the P4 thought none of the others would ever catch up in any season. This was supposed to be their way of cementing themselves but a couple of teams dropped the ball.